[lammps-users] Lost Atoms

Hi, LAMMPSians,

I tried to simulate irradiation with LAMMPS, but it broke down at timestep 2070000 and appeared “Error: Lost atoms: original 4043 current 3372”. The attached file is the picture of last two frames and my in script. The grey atoms is of the previous frame, and the yellow the latter. A ribbon of atoms have disappeared. It seems to lost all atoms of some processors. I’ve no idea of the reason. Would you give me advice about how to do with this problem?

The boundary is s s s, and i write an “irradiate” fix to delete atoms out of defined region. The new fix runs successfully before the timestep 2070000, and has deleted atoms from 4086 to 4035 at timestep 2060000.

Thank you very much!

Wenpeng Zhu

2010-03-31

LostAtoms.JPG

log.lammps (22.5 KB)

in.graphene.relax (1.63 KB)

I don't know. Presumably the fix you added is messing something up,
so you'll have to debug it.

I also presume you are using thermo_modify lost ignore?
I would probably run with a memory checker on, like valgrind,
and see if shorter, smaller runs, with a few deletion steps
run cleanly, both in serial and in parallel.

Steve

2010/3/30 Wenpeng Zhu <[email protected]>: